Add files via upload

nicholascwho · Jun 29, 2023 · a8fc25a · a8fc25a
1 parent 368e61c
commit a8fc25a
Showing 1 changed file with 13 additions and 0 deletions.
diff --git a/HNSCC Explant on Hydrogel 2023/STAR script.sh b/HNSCC Explant on Hydrogel 2023/STAR script.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+for i in `ls`; 
+do 
+zcat $i/*1.fq.gz >> ../combined/$i.1.fq; 
+echo $i.1 ;
+zcat $i/*2.fq.gz >> ../combined/$i.2.fq;
+echo $i.2 ; 
+STAR --genomeDir ../NCBI_hg38_star_149bp_overhang --runThreadN 24 --readFilesIn ../combined/$i.1.fq ../combined/$i.2.fq --outFileNamePrefix ../result/$i/$i_ --sjdbOverhang 149 --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM GeneCounts;
+echo $i
+rm ../combined/$i.1.fq ../combined/$i.2.fq;
+rm $i/*1.fq.gz $i/*2.fq.gz;
+done